Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database

By Brigitte Courtois, Nourollah Ahmadi, F. Khowaja, Alkes L Price, J. Rami, J. Frouin, Chantal Hamelin, M. Ruiz. Rice, 2009

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During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number, maximum root length, root thickness, root/shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published between 1995 and 2007. The physical position on the pseudo-chromosomes of the markers flanking each QTL was determined. An overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of “hot spots,” The 32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones, encompassed only a few genes.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/bfff3ff3ac3372d494eec8643692e5c409d71d84

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Citations in the corpus

Recent Updates on Salinity Stress in Rice: From Physiological to Molecular Responses (2011, methodology): “fr) following a procedure identical to that used to compile QTLs of drought tolerance (Courtois et al., 2009).”
Root biology and genetic improvement for drought avoidance in rice (2011, methodology): “Rice root QTLs for drought have been compiled using QTL meta-analysis in multiple populations (Norton et al., 2008; Courtois et al., 2009).”
A consensus map of QTLs controlling the root length of maize (2011, methodology): “This approach was used to detect meta-QTLs for Fusarium head blight resistance of wheat (Triticum aestivum L.) (Loffler et al. 2009), for virus resistance of apricots (Prunus armeniaca L.) (Marandel et al. 2009) and root architecture in rice (Oryza sativa L.) (Courtois et al. 2009).”
Root traits contributing to plant productivity under drought (2013, background): “These include in rice: increased root length (Price et al., 2002; MacMillan et al., 2006; Courtois et al., 2009), root biomass (Courtois et al., 2003), and root number (Zheng et al., 2000, 2003; Courtois et al., 2009); in wheat: increased total root biomass, length and number of roots (Sharma et…”